Institutional Data Repository Research Articles

Seek and you may (not) find: A multi-institutional analysis of where research data are shared.

Research data sharing has become an expected component of scientific research and scholarly publishing practice over the last few decades, due in part to requirements for federally funded research. As part of a larger effort to better understand the workflows and costs of public access to research data, this project conducted a high-level analysis of where academic research data is most frequently shared. To do this, we leveraged the DataCite and Crossref application programming interfaces (APIs) in search of Publisher field elements demonstrating which data repositories were utilized by researchers from six academic research institutions between 2012-2022. In addition, we also ran a preliminary analysis of the quality of the metadata associated with these published datasets, comparing the extent to which information was missing from metadata fields deemed important for public access to research data. Results show that the top 10 publishers accounted for 89.0% to 99.8% of the datasets connected with the institutions in our study. Known data repositories, including institutional data repositories hosted by those institutions, were initially lacking from our sample due to varying metadata standards and practices. We conclude that the metadata quality landscape for published research datasets is uneven; key information, such as author affiliation, is often incomplete or missing from source data repositories and aggregators. To enhance the findability, interoperability, accessibility, and reusability (FAIRness) of research data, we provide a set of concrete recommendations that repositories and data authors can take to improve scholarly metadata associated with shared datasets.

Risky Business: Data-At-Risk in a Dynamic and Evolving Multidisciplinary Research Environment

At-risk data is an unfortunate research reality and can be present in all data formats in a range of research disciplines. This is defined as data that are at risk of loss due to various factors, including deterioration of the media, lack of accompanying documentation and data that exists in non-digital formats, which are often irreplaceable. Continued access to older data has a range of benefits. The factors that place valuable data at risk are therefore a cause for concern. This paper reports on a multi-method case study, comprising a survey and interviews. A web-based questionnaire was distributed to all research group leaders based at a leading South African research institute. This was followed by one-on-one interviews that were held with a sub-section of the same group of researchers. The combined findings of the two methods enabled a picture to be formed regarding factors that jeopardise research data, data rescue obstacles that the researchers encountered and the state of data rescue at the institute. Several recommendations and strategies are put forward to address identified risk factors and challenges. Suggestions include the launch of a data rescue project, awareness training around data at risk, involving the institute’s library and information services (LIS) section in data rescue and launching continued efforts to acquire a dedicated institutional data repository. It is also important to ensure that the scope of project risk management includes data considerations. The combined implementation of recommendations is anticipated to ensure the accessibility and usability of older at-risk data and reduce the chances of current and future data becoming compromised.

Searches as data: archiving and sharing search strategies using an institutional data repository

Background: By defining search strategies and related database exports as code/scripts and data, librarians and information professionals can expand the mandate of research data management (RDM) infrastructure to include this work. This new initiative aimed to create a space in McGill University’s institutional data repository for our librarians to deposit and share their search strategies for knowledge syntheses (KS). Case Presentation: The authors, a health sciences librarian and an RDM specialist, created a repository collection of librarian-authored knowledge synthesis (KS) searches in McGill University’s Borealis Dataverse collection. We developed and hosted a half-day “Dataverse-a-thon” where we worked with a team of health sciences librarians to develop a standardized KS data management plan (DMP), search reporting documentation, Dataverse software training, and how-to guidance for the repository. Conclusion: In addition to better documentation and tracking of KS searches at our institution, the KS Dataverse collection enables sharing of searches among colleagues with discoverable metadata fields for searching within deposited searches. While the initial creation of the DMP and documentation took about six hours, the subsequent deposit of search strategies into the institutional data repository requires minimal effort (e.g., 5-10 minutes on average per deposit). The Dataverse collection also empowers librarians to retain intellectual ownership over search strategies as valuable stand-alone research outputs and raise the visibility of their labor. Overall, institutional data repositories provide specific benefits in facilitating compliance both with PRISMA-S guidance and with RDM best practices.

Robot assisted Laparoscopic Cholecystectomy- A Comparative study

Background- Robotic surgery has recently grown in acceptance and usefulness in general surgery, and it may offer superior results to laparoscopic surgery in some gastrointestinal operations. Objectives- To assess if the use of robot assistance during laparoscopic cholecystectomy is warranted when compared to traditional laparoscopic cholecystectomy. Methods- It was a retrospective record based study. All patients undergoing robotic or laparoscopic cholecystectomy between 2019 and 2022 at a single academic medical center were captured using institutional data. A total of 110 robotic surgeries were done and 1200 Laparoscopic cholecystectomies was done during the study period. The bulk of cases were primarily handled by two acute care general surgeons, who also conducted robotic and laparoscopic cholecystectomies. The institutional Clinical Data Repository provided the financial information. The study was approved by Institutional Ethics Committee. Age, sex, race, body mass index (BMI), and comorbid conditions of the patient were examined prior to surgery. SPSS was used for analysis. Results- A total of 1310 patients were identified who underwent robotic or laparoscopic cholecystectomy between 2019 and 2022 among them Robotic-assisted approach was used in 9.1% (n = 110) of cases. There were no demographic differences in age, sex, race, and body mass index (BMI). Type II diabetes mellitus, hypertension, and CHF disease were statistically significantly different between groups. Mean age (Robotic: 41 [29-56] vs. Laparoscopic: 43 [30-54] years, p = 0.11) and BMI (Robotic: 28.4 [26.6-32.4] vs. Laparoscopic: 29.2 [27.5-33.4]) were similar between groups. both operative duration was greater and hospital cost were greater in robotic-assisted cholecystectomy and it was statistically significant (p<0.05), but hospital duration of stay and 90-day related readmission rates were less in robotic-assisted cholecystectomy which was significant; 30-day readmission rates were similar between both groups. Conclusion- When compared to laparoscopic cholecystectomy, robotic cholecystectomy has longer operating times and higher hospital costs, but it is also related with shorter hospital stays and a lower readmission rate within 90 days after the index procedure. Before exploring robotic cholecystectomy, hospitals and surgeons must weigh the enhanced clinical outcomes against the time and money necessary.

Investigating and understanding library data services to support college student data literacy competencies: A conceptual framework

Guided by a conceptual framework based on the baseline data literacy competencies (DLCs) mapped to the ACRL information literacy framework and the extended technology acceptance model, this study uses an online survey to investigate the factors related to student users’ potential acceptance of library data services supporting DLCs in a master’s college environment. With quantitative and qualitative data analyses, the study builds three conceptual models to demonstrate how students’ study-related data engagement and backgrounds may influence their attitudes toward multi-aspect library data services, including general data services, an institutional data repository, if available, as a data resource, and institutional data repository-based services. The study’s findings support library data services’ cross-disciplinary, multidimensional, and multilevel nature, addressing the value of institutional data repositories and repository-based data services in comprehensively promoting data literacy competencies of all groups in all disciplines. The contribution of this study, beyond being among the first to look at library data services from a holistic perspective to support college students’ DLCs, includes a call for further explorations of student data engagement practice and verifying and generalizing the current study findings by investigating more students’ data services need in more college communities.

Risk of severe toxicity from topical fluoropyrimidine treatment in patients carrying DPYD variant alleles.

12123 Background: Patients carrying variant alleles of DPYD that reduce activity of dihydropyrimidine dehydrogenase have unacceptably high risk of severe toxicity from systemic fluoropyrimidine chemotherapy. DPYD testing prior to systemic fluoropyrimidine treatment is standard of care across Europe and is increasingly used in USA. There is a published case report of fatal toxicity from topical fluoropyridine chemotherapy in a DPYD variant carrier, but the risk of severe toxicity in these patients is unknown. This information is critical to determine whether patients receiving topical fluoropyrimidine treatment should also undergo DPYD genetic testing. The objective of this retrospective cohort study was to determine whether patients carrying DPYD variant alleles have increased risk of severe toxicity from topical fluoropyrimidine treatment. Methods: Individuals who received topical fluoropyrimidine treatment at Michigan Medicine and had available DPYD genotype data, due to participation in the Michigan Genomics Initiative institutional genetic data repository, were eligible for this analysis. Clinical data for the first cycle of topical fluoropyrimidine treatment was abstracted from the electronic medical record by an investigator blinded to genetic data. Toxicities were graded based on the Common Terminology Criteria for Adverse Events (CTCAE) version 5.0. The primary endpoint was grade 3+ toxicity. The secondary endpoint was grade 1+ toxicity. Genotypes for five validated decreased- or null-activity DPYD variant alleles were included: DPYD*2A (rs3918290), DPYD*13 (rs55886062), DPYD p.D949V (rs67376798) DPYD HapB3 (rs56038477) and DPYD p.Y186C (rs115232898). Toxicity rates in DPYD variant carriers vs. wild-type were compared using Fisher’s Exact tests. Results: 201 patients receiving topical fluoropyrimidine therapy who had available DPYD genotype data were included in the analysis. Most patients were self-reported white (97%), male (71%), and received topical fluoropyrimidine for a diagnosis of actinic keratosis (79%). As expected in a US patient cohort, 7.0% (14/201) of patients carried a DPYD variant. No patients experienced grade 3+ toxicity. Patients carrying a DPYD variant allele had nominally higher risk of grade 1+ toxicity (21.4% vs. 10.2%, odds ratio = 2.40 (95% Confidence Interval: 0.10-2.53), p = 0.19). Conclusions: Patients carrying DPYD variant alleles may have increased risk of non-severe toxicity from topical fluoropyrimidines, but the risk of severe toxicity is minimal regardless of genotype. DPYD genetic testing to prevent severe and fatal fluoropyrimidine toxicity should be reserved for patients receiving systemic treatment and need not include patients receiving topical treatment, in whom risk of severe toxicity is minimal.

Confirmatory DPYD Testing in Patients Receiving Fluoropyrimidines Who are Suspected DPYD Variant Carriers Based on a Genetic Data Repository.

Using pharmacogenetics (PGx) to inform clinical decision making can benefit patients but clinical use of PGx testing has been limited. Existing genetics data obtained in the course of research could be used to identify patients who are suspected, but have not yet been confirmed, to carry clinically actionable genotypes, in whom confirmatory genetic testing could be conducted for highly efficient PGx implementation. Herein, we demonstrate that it is regulatorily and technically feasible to implement PGx by identifying suspected carriers of actionable genotypes within an institutional genetics data repository and conduct confirmatory PGx testing immediately prior to that patient receiving the PGx-relevant drug, using a case study of DPYD testing prior to fluoropyrimidine chemotherapy. In 2 years since launching this program, ~ 3,000 suspected DPYD carriers have been passively monitored and one confirmed DPYD carrier was prevented from receiving unacceptably toxic fluoropyrimidine treatment, for minimal cost and effort. Now that we have demonstrated the feasibility of this strategy, we plan to transition to PGx panel testing and expand implementation to other genes and drugs for which the evidence of clinical benefit of PGx-informed treatment is high but PGx testing is not generally conducted. This highly efficient implementation process will maximize the clinical benefits of testing and could be explored at other institutions that have research-only genetic data repositories to expand the number of patients who benefit from PGx-informed treatment while we continue to work toward wide-scale adoption of PGx testing and implementation.

Data sharing attitudes and practices of researchers in Korean government research institutes: a survey-based descriptive study

Purpose: This study explored to what extent and how researchers in five Korean government research institutes that implement research data management practices share their research data and investigated the challenges they perceive regarding data sharing.Methods: The study collected survey data from 224 respondents by posting a link to a SurveyMonkey questionnaire on the homepage of each of the five research institutes from June 15 to 29, 2022. Descriptive statistical analyses were conducted.Results: Among 148 respondents with data sharing experience, the majority had shared some or most of their data. Restricted data sharing within a project was more common than sharing data with outside researchers on request or making data publicly available. Sharing data directly with researchers who asked was the most common method of data sharing, while sharing data via institutional repositories was the second most common method. The most frequently cited factors impeding data sharing included the time and effort required to organize data, concerns about copyright or ownership of data, lack of recognition and reward, and concerns about data containing sensitive information.Conclusion: Researchers need ongoing training and support on making decisions about access to data, which are nuanced rather than binary. Research institutes’ commitment to developing and maintaining institutional data repositories is also important to facilitate data sharing. To address barriers to data sharing, it is necessary to implement research data management services that help reduce effort and mitigate concerns about legal issues. Possible incentives for researchers who share data should also continue to be explored.

French Biodiversity Data Hub: Linking local to global biodiversity through international initiatives and open science clouds

The French national biodiversity data hub (“Pôle National de Données de Biodiversité” - PNDB) is a national e-infrastructure created in 2018 and led by the National Museum of Natural History, contributing to the Open Science policy of the Ministry of Higher Education, Research and Innovation (MESRI). PNDB contributes to building an integrative framework taking into account biodiversity over the long term (from the origins of life to future models), at all biological scales (from the molecule to the socio-ecosystem), and in all its interactions, by providing tools and services for the description, access, validation, analysis and reuse of biodiversity data. With the diversity and complementary type of research biodiversity data (information systems, institutional data repositories, research infrastructures as observatories, experimental devices, natural history collections, etc.), but also from public policy data, the missions of the PNDB are deeply based on the FAIR approach (making data Findable, Accessible, Interoperable, Reusable). Thanks to its nomination in 2022 as a thematic reference center of the MESRI, PNDB will contribute to promoting the FAIR approach, will increase the skills (e.g., by training, good practices) of the scientific communities around open science, and stimulate interactions between producers and users of biodiversity data. PNDB has led the French participation to GEO BON (Group on Earth Observations Biodiversity Observation Network) since 2018 and recently shared the lead with public policies information system coordination. Thanks to this co-lead, this national BON proposes an innovative coordination of all biodiversity monitoring programs, from expertise to research around an innovative Essential Biodiversity Variable (EBV) operationalization pilot. This pilot is made of open practical solutions providing a particular high degree of FAIRNess of biodiversity research objects, from data to source codes. PNDB is also a major European point of contact for the DataOne network, who, in combination with the strong link between PNDB and French Global Biodiversity Information Facility (GBIF) node colleagues, allows the dissemination of all types of data through the world in the best manner!

A multi-stakeholder participatory pilot study of the data demands of the future Ethiopian dairy sector.

Background: This paper describes a pilot study undertaken in 2018, to determine the key data needs of each of the different Ethiopian dairy sector stakeholder groups. The study aimed to characterise the emerging trends of dairy product production, processing, retailing and consumption in Ethiopia, and to identify and characterise current and future data needs of different stakeholders. Methods: The study undertook a mapping of the interactions between different stakeholders in the dairy sector, and an interactive evaluation of the institutional data repository and access options. Focus group discussions and interviews were held in three regions of the country prior to a two-day workshop in the capital Addis Ababa. Data needs were characterised by type, availability, format, level of detail, methods of dissemination, uptake and use, and the institutional arrangement, including the different roles of public and private sectors in decision making processes. Results: The study highlighted the main data needs and identified several broader institutional issues constraining the further development of the Ethiopian dairy sector. The stakeholder groups endorsed the reactivation of a national dairy board, independent of government but closely incorporating government, and with the buy-in and membership of private sector enterprises, including producers, processers, service providers and consumers, to provide clearer facilitative leadership on the dairy industry. Conclusions: The study workshop provided a timely discussion between diverse stakeholders, including government, and several potential organisations were suggested to host and manage a national dairy database. Importantly, the reactivation of a national dairy board was strongly endorsed. It was recommended that stakeholder links be established, sector-specific data needs be elevated to higher detail, and a national roll out of herd-specific data recording schemes was called for, to allow for effective evidence-based policies and decision making.

Is the ocean science data repository, JOISS able to be FAIR?

As the global open science movement has recently proven its effectiveness in responding to the corona pandemic, research on disciplinary or institutional data repositories and establishing service platforms for the open and sharing research data are also active in Korea. The purpose of the research data repository is not to manage data per se but to discover and innovate knowledge and to integrate and reuse subsequent data and knowledge. Therefore, recent repository-related studies emphasize implementing the FAIR principle in this collaborative process, from observation to data documentation, data combination, quality control, and data publication. In particular, high-level data interoperability through the FAIR implementation of the repository is essential for ocean observation that requires multidisciplinary collaborative research. In Korea, ocean observatory organizations have repositories, including the ocean science data repository, JOISS; however, no studies evaluate the establishment and operation of data repositories in the FAIR principle. Therefore, this study aims to examine the construction process and data management status of the JOISS repository and the main functions and services of the web platform in terms of the data lifecycle and evaluate The FAIR principle of Open Science works in such an operating system and its limitations. The study provides implications for the improvement direction of data management and services of domestic marine repositories, including the JOISS, in an environment where the diversity and volume of data are rapidly increasing along with the evolution of ocean observation.

A multi-stakeholder participatory pilot study of the data demands of the future Ethiopian dairy sector

Background: This paper describes a pilot study undertaken in 2018, to determine the key data needs of each of the different Ethiopian dairy sector stakeholder groups. The study aimed to characterise the emerging trends of dairy product production, processing, retailing and consumption in Ethiopia, and to identify and characterise current and future data needs of different stakeholders. Methods: The study undertook a mapping of the interactions between different stakeholders in the dairy sector, and an interactive evaluation of the institutional data repository and access options. Focus group discussions and interviews were held in three regions of the country prior to a two-day workshop in the capital Addis Ababa. Data needs were characterised by type, availability, format, level of detail, methods of dissemination, uptake and use, and the institutional arrangement, including the different roles of public and private sectors in decision making processes. Results: The study highlighted the main data needs and identified several broader institutional issues constraining the further development of the Ethiopian dairy sector. The stakeholder groups endorsed the reactivation of a national dairy board, independent of government but closely incorporating government, and with the buy-in and membership of private sector enterprises, including producers, processers, service providers and consumers, to provide clearer facilitative leadership on the dairy industry. Conclusions: The study workshop provided a timely discussion between diverse stakeholders, including government, and several potential organisations were suggested to host and manage a national dairy database. Importantly, the reactivation of a national dairy board was strongly endorsed. It was recommended that stakeholder links be established, sector-specific data needs be elevated to higher detail, and a national roll out of herd-specific data recording schemes was called for, to allow for effective evidence-based policies and decision making.

Lack of association of CYP2B6 pharmacogenetics with cyclophosphamide toxicity in patients with cancer.

Cyclophosphamide is a commonly used cancer agent that is metabolically activated by polymorphic enzymes. This study aims to investigate the association between predicted activity of candidate pharmacogenes with severe toxicity during cyclophosphamide treatment. Genome-wide genetic data was collected from an institutional genetic data repository for CYP2B6, CYP3A4, CYP2C9, CYP2C19, GSTA1, GSTP1, ALDH1A1, ALDH3A1, ABCC1, ABCB1, and ERCC1. Treatment and toxicity data were retrospectively collected from the patient's medical record. The a priori selected primary hypothesis was that patients who have CYP2B6 reduced metabolizer activity (poor or intermediate (PM/IM) vs. normal (NM) metabolizer) have lower risk of severe toxicity or cyclophosphamide treatment modification due to toxicity. In the primary analysis of 510 cyclophosphamide-treated patients with available genetic data, there was no difference in the odds of severe toxicity or treatment modification due to toxicity in CYP2B6 PM/IM vs. NM (odds ratio = 0.97, 95% Confidence Interval: 0.62-1.50, p = 0.88). In an exploratory, statistically uncorrected secondary analysis, carriers of the ALDH1A1 rs8187996 variant had a lower risk of the primary toxicity endpoint compared with wild-type homozygous patients (odds ratio = 0.31, 95% Confidence Interval: 0.09-0.78, p = 0.028). None of the other tested phenotypes or genotypes was associated with the primary or secondary endpoints in unadjusted analysis (all p > 0.05). The finding that patients who carry ALDH1A1 rs8187996 may have a lower risk of cyclophosphamide toxicity than wild-type patients contradicts a prior finding for this variant and should be viewed with skepticism. We found weak evidence that any of these candidate pharmacogenetic predictors of cyclophosphamide toxicity may be useful to personalize cyclophosphamide dosing to optimize therapeutic outcomes in patients with cancer.

A multi-stakeholder participatory pilot study of the data demands of the future Ethiopian dairy sector

Background: This paper describes a pilot study undertaken in 2018, to determine the key data needs of each of the different Ethiopian dairy sector stakeholder groups. The study aimed to characterise the emerging trends of dairy product production, processing, retailing and consumption in Ethiopia, and to identify and characterise current and future data needs of different stakeholders. Methods: The study undertook a mapping of the interactions between different stakeholders in the dairy sector, and an interactive evaluation of the institutional data repository and access options. Focus group discussions and interviews were held in three regions of the country prior to a two-day workshop in the capital Addis Ababa. Data needs were characterised by type, availability, format, level of detail, methods of dissemination, uptake and use, and the institutional arrangement, including the different roles of public and private sectors in decision making processes. Results: The study highlighted the main data needs and identified several broader institutional issues constraining the further development of the Ethiopian dairy sector. The stakeholder groups endorsed the reactivation of a national dairy board, independent of government but closely incorporating government, and with the buy-in and membership of private sector enterprises, including producers, processers, service providers and consumers, to provide clearer facilitative leadership on the dairy industry. Conclusions: The study workshop provided a timely discussion between diverse stakeholders, including government, and several potential organisations were suggested to host and manage a national dairy database. Importantly, the reactivation of a national dairy board was strongly endorsed. It was recommended that stakeholder links be established, sector-specific data needs be elevated to higher detail, and a national roll out of herd-specific data recording schemes was called for, to allow for effective evidence-based policies and decision making.

Protocol for updated systematic review and meta-analysis on the burden of non-communicable diseases among people living with HIV in sub-Saharan Africa

IntroductionSub-Saharan Africa (SSA) is faced with the dual epidemics of HIV/AIDS and non-communicable diseases (NCDs). Cardiovascular diseases, cancers, chronic respiratory diseases, diabetes and mental illnesses are the five major NCDs,...

A pilot study of the data demands of different stakeholders for the future Ethiopian dairy sector

Background: This paper describes a pilot study undertaken in 2018, to determine the key data needs of each of the different Ethiopian dairy sector stakeholder groups. The study aimed to characterise the emerging trends of dairy product production, processing, retailing and consumption in Ethiopia, and to identify and characterise current and future data needs of different stakeholders. Methods: The study undertook a mapping of the interactions between different stakeholders in the dairy sector, and an interactive evaluation of the institutional data repository and access options. Focus group discussions and interviews were held in three regions of the country prior to a two-day workshop in the capital Addis Ababa. Data needs were characterised by type, availability, format, level of detail, methods of dissemination, uptake and use, and the institutional arrangement, including the different roles of public and private sectors in decision making processes. Results: The study highlighted the main data needs and identified several broader institutional issues constraining the further development of the Ethiopian dairy sector. The stakeholder groups endorsed the reactivation of a national dairy board, independent of government but closely incorporating government, and with the buy-in and membership of private sector enterprises, including producers, processers, service providers and consumers, to provide clearer facilitative leadership on the dairy industry. Conclusions: The study workshop provided a timely discussion between diverse stakeholders, including government, and several potential organisations were suggested to host and manage a national dairy database. Importantly, the reactivation of a national dairy board was strongly endorsed. It was recommended that stakeholder links be established, sector-specific data needs be elevated to higher detail, and a national roll out of herd-specific data recording schemes was called for, to allow for effective evidence-based policies and decision making.

Technical Considerations for a Transactional Model to Realize the Digital Extended Specimen

Technological innovations over the past two decades have given rise to the online availability of more than 150 million specimen and species-lot records from biological collections around the world through large-scale biodiversity data-aggregator networks. In the present landscape of biodiversity informatics, collections data are captured and managed locally in a wide variety of databases and collection management systems and then shared online as point-in-time Darwin Core archive snapshots. Data providers may publish periodic revisions to these data files, which are retrieved, processed and re-indexed by data aggregators. This workflow has resulted in data latencies and lags of months to years for some data providers. The Darwin Core Standard Wieczorek et al. (2012) provides guidelines for representing biodiversity information digitally, yet varying institutional practices and lack of interoperability between Collection Management Systems continue to limit semantic uniformity, particularly with regard to the actual content of data within each field. Although some initiatives have begun to link data elements, our ability to comprehensively link all of the extended data associated with a specimen, or related specimens, is still limited due to the low uptake and usage of persistent identifiers. The concept now under consideration is to create a Digital Extended Specimen (DES) that adheres to the tenets of Findable, Accessible, Interoperable and Reusable (FAIR) data management of stewardship principles and is the cumulative digital representation of all data, derivatives and products associated with a physical specimen, which are individually distinguished and linked by persistent identifiers on the Internet to create a web of knowledge. Biodiversity data aggregators that mobilize data across multiple institutions routinely perform data transformations in an attempt to provide a clean and consistent interpretation of the data. These aggregators are typically unable to interact directly with institutional data repositories, thereby limiting potentially fruitful opportunities for annotation, versioning, and repatriation. The ability to track such data transactions and satisfy the accompanying legal implications (e.g. Nagoya Protocol) is becoming a necessary component of data publication which existing standards do not adequately address. Furthermore, no mechanisms exist to assess the “trustworthiness” of data, critical to scientific integrity, reproducibility or to provide attribution metrics for collections to advocate for their contribution or effectiveness in supporting such research. Since the introduction of Darwin Core Archives Wieczorek et al. (2012) little has changed in the underlying mechanisms for publishing natural science collections data and we are now at a point where new innovations are required to meet current demand for continued digitization, access, research and management. One solution may involve changing the biodiversity data publication paradigm to one based on the atomized transactions relevant to each individual data record. These transactions, when summed over time, allows us us to realize the most recently accepted revision as well as historical and alternative perspectives. In order to realize the Digital Extended Specimen ideals and the linking of data elements, this transactional model combined with open and FAIR data protocols, application programming interfaces (APIs), repositories, and workflow engines can provide the building blocks for the next generation of natural science collections and biodiversity data infrastructures and services. These and other related topics have been the focus of phase 2 of the global consultation on converging Digital Specimens and Extended Specimens. Based on these discussions, this presentation will explore a conceptual solution leveraging elements from distributed version control, cryptographic ledgers and shared redundant storage to overcome many of the shortcomings of contemporary approaches.

Ibrutinib in Steroid-Refractory Chronic Graft-versus-Host Disease, a Single-Center Experience

Chronic graft-versus-host disease (cGVHD) is a leading cause of late morbidity and mortality after allogenic hematopoietic stem cell transplantation. Corticosteroid-based therapies are a mainstay of its initial treatment but there is no consensus in how to treat steroid-refractory cGVHD. Ibrutinib is a Bruton tyrosine kinase and IL-2-inducible kinase inhibitor thought to affect pathways driving cGVHD, and it was approved for the treatment of refractory cGVHD by the Food and Drug Administration (FDA) in August 2017 after a landmark phase 1b/2 study. It was the first medication approved for this indication, but how to best treat refractory cGVHD remains an open question, and there has been limited literature on ibrutinib after the FDA approval. This study sought to characterize the utilization and outcomes associated with ibrutinib use in cGVHD via a retrospective single-center study. Fifty-three patients were identified as having been treated with ibrutinib for cGVHD following FDA approval between September 1, 2017, and December 31, 2020, using an institutional data repository. Their records were reviewed for demographics, cGVHD characteristics, and outcomes. For the entire cohort, two-year overall survival was 76% (95% confidence interval [CI], 60% to 86%), with a median follow-up among survivors of 26 months (range, 1.3 to 39.5 months). However, the 2-year failure-free survival (FFS) after initiation of ibrutinib was 9% (95% CI, 2.6% to 20%), and the median FFS was 4.5 months (95% CI, 2.8 to 7.1 months). Events of FFS included treatment change due to lack of response or toxicity, malignant relapse, or non-treatment related mortality. At the time of this report, 11 patients (21%) remained on ibrutinib. At the time of the FFS event or last follow-up, 6 patients (12%) had a complete or partial response, 34 (64%) had stable disease, and 13 (25%) had progressive disease. Ibrutinib use was associated with no reduction in corticosteroid dose between ibrutinib initiation and FFS event or last follow-up (mean difference, 0.00; P=.98). The most frequently used noncorticosteroid cGVHD therapy after ibrutinib was ruxolitinib (n=14; 33%). The most common adverse events associated with treatment discontinuation were infection (lung, skin, enterocolitis; n=6), bleeding and bruising (hematoma, epistaxis, gastrointestinal bleed; n=5), and muscle aches (n=2). In a real-world setting, ibrutinib is associated with a modest response rate and FFS and its use in a narrower, more targeted patient population may be indicated.

Are data repositories fettered? A survey of current practices, challenges and future technologies

PurposeThe purpose of this study is to explore current practices, challenges and technological needs of different data repositories.Design/methodology/approachAn online survey was designed for data repository managers, and contact information from the re3data, a data repository registry, was collected to disseminate the survey.FindingsIn total, 189 responses were received, including 47% discipline specific and 34% institutional data repositories. A total of 71% of the repositories reporting their software used bespoke technical frameworks, with DSpace, EPrint and Dataverse being commonly used by institutional repositories. Of repository managers, 32% reported tracking secondary data reuse while 50% would like to. Among data reuse metrics, citation counts were considered extremely important by the majority, followed by links to the data from other websites and download counts. Despite their perceived usefulness, repository managers struggle to track dataset citations. Most repository managers support dataset and metadata quality checks via librarians, subject specialists or information professionals. A lack of engagement from users and a lack of human resources are the top two challenges, and outreach is the most common motivator mentioned by repositories across all groups. Ensuring findable, accessible, interoperable and reusable (FAIR) data (49%), providing user support for research (36%) and developing best practices (29%) are the top three priorities for repository managers. The main recommendations for future repository systems are as follows: integration and interoperability between data and systems (30%), better research data management (RDM) tools (19%), tools that allow computation without downloading datasets (16%) and automated systems (16%).Originality/valueThis study identifies the current challenges and needs for improving data repository functionalities and user experiences.Peer reviewThe peer review history for this article is available at: https://publons.com/publon/10.1108/OIR-04-2021-0204

Implementing and Managing a Data Curation Workflow in the Cloud

Objective: To increase data quality and ensure compliance with appropriate policies, many institutional data repositories curate data that is deposited into their systems. Here, we present our experience as an academic library implementing and managing a semi-automated, cloud-based data curation workflow for a recently launched institutional data repository. Based on our experiences we then present management observations intended for data repository managers and technical staff looking to move some or all of their curation services to the cloud. Methods: We implemented tooling for our curation workflow in a service-oriented manner, making significant use of our data repository platform’s application programming interface (API). With an eye towards sustainability, a guiding development philosophy has been to automate processes following industry best practices while avoiding solutions with high resource needs (e.g., maintenance), and minimizing the risk of becoming locked-in to specific tooling. Results: The initial barrier for implementing a data curation workflow in the cloud was high in comparison to on-premises curation, mainly due to the need to develop in-house cloud expertise. However, compared to the cost for on-premises servers and storage, infrastructure costs have been substantially lower. Furthermore, in our particular case, once the foundation had been established, a cloud approach resulted in increased agility allowing us to quickly automate our workflow as needed. Conclusions: Workflow automation has put us on a path toward scaling the service and a cloud based-approach has helped with reduced initial costs. However, because cloud-based workflows and automation come with a maintenance overhead, it is important to build tooling that follows software development best practices and can be decoupled from curation workflows to avoid lock-in.